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I have a home HVAC system that is zoned into two zones. One zone runs the first floor and basement and the other runs the second floor. I am replacing both the furnace and the a/c. The salesman tells me that a two-speed furnace is more appropriate for zoned systems than a variable speed. Is that correct? I'm also looking at replacing both thermostats with digital programmable units. I know I need to buy a two-stage compatible thermostat, but will I run into any other problems considering this is a two-zoned system? Thanks much!

2 stage furnaces are fine with zoning but often that benefit is lost because most zone panels don't know how to handle them. We have a Zonex 4+2 panel which will bring the high fire on based on time but reduce it to low if the temp gets too warm with 1 zone calling. It's happy to run steadily on low all day if need be. But most panels will cycle the furnace off for a few minutes then back on low then high then off. That's very inefficient. I was talking to a Honeywell man last night, that's how their better panel does it. I wouldn't like that.

Some of the controls made to match a certain brand will offer better control of the staging. Carrier's Infinity probably would, not sure on the Lennox Harmony.

The EWC brand UZC3 zone control, and I assume other manufacturers 3 zone controls, can be set so that they will never call for 2nd stage heating or cooling if less than 50% of the zones are calling.
It is a 3 zone panel, so if you have only 2 zones, it will never call for 2nd stage if only one zone is calling.
You can also use standard 1h/1c thermostats with it.

Also, most furnaces with varriable speed blowers are also 2 stage heating.

If you are not mistaken about what the salesman is telling you about two stage vs. variable speed then I would suggest calling a new company! As already stated in post by other people a 2 stage can or can not be useful depending on the controls. Also A variable speed blower is a must in any zone system I install......but the two things are different issues its not a matter of one over the other. That is why I suggest calling a new company.

If you are zoning a system that just shuts down certain zones when they are not calling then you should probably look for a blower that will maintain a pressure differential across the blower these fans are usually a DC motor in residential applications I know that RHEEM makes one it works very well with zoned systems that do not bypass air back to the return ( which is a crummy way of doing it).